pymol

Launch a PyMOL session via pymol-agent-bridge for molecular visualization and image export.

3|Updated Jan 28, 2026

Search Tags:#automation #integration #cli #structure #visualization #session #pymol

Ready to run

npx skills add https://github.com/ANaka/claudemol --skill pymol

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pymol
Source: https://github.com/ANaka/claudemol/tree/main/claude-plugin/skills/pymol
Command: npx skills add https://github.com/ANaka/claudemol --skill pymol

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Establish a smooth, reliable PyMOL session workflow from Claude, enabling quick visualization and interactive manipulation of molecular structures without manual setup.

Core Features & Use Cases

pymol-fundamentals - Basic visualization, selections, representations
pymol-setup - First-time configuration and environment setup
structure-alignment-analysis - Structure comparisons and alignment
publication-figures - High-quality figure export for publications
binding-site-visualization - Protein-ligand binding site insights
miscellaneous - Additional PyMOL utility commands

Quick Start

Run /pymol-setup to install and configure the bridge, then ask Claude to launch and connect to a PyMOL session via the pymol-agent-bridge.

Frequently Asked Questions about pymol

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I control PyMOL molecular visualization from Claude?▼

You can control PyMOL visualization from Claude by launching the pymol-agent-bridge to establish a socket connection for manipulating molecular structures, selections, and representations.

What do I need to set up before automating PyMOL sessions with Claude?▼

To automate PyMOL sessions, you need to run the initial setup to install the pymol-agent-bridge and configure your PyMOL environment, ensuring a stable socket connection for structure visualization.

Can I generate publication-quality figures of protein structures using Claude?▼

Yes, you can generate publication-quality figures by instructing Claude to apply specific representations and export high-quality images of your molecular structures directly through the active PyMOL session.

How does Claude handle protein-ligand binding site visualization in PyMOL?▼

Claude handles binding site visualization by sending commands through the pymol-agent-bridge to create specific selections and representations, allowing you to visualize protein-ligand interactions without manual setup.

Why does my Claude PyMOL session keep disconnecting during structure manipulation?▼

Session disconnections during structure manipulation often occur if the pymol-agent-bridge is not properly configured or the socket connection is unstable, requiring you to verify your environment setup and reconnect.